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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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Question about bps4IS #21

Closed Gonzalez-toro closed 2 years ago

Gonzalez-toro commented 4 years ago

Hi xie First of all thanks for ISEScan. I have doubts regarding the meaning of bps4IS. If you could briefly explain what that value means, I would appreciate it, because it is not clear to me with the explanation and I looked in the article and did not find the term and on the other hand could you tell me how this parameter was defined.

Regards and thanks

xiezhq commented 4 years ago

Thanks for your interest with ISEScan. Le't use a simple example to explain it. If we have a sequence dnaseq and the length is 5k (1-5000). ISEScan reports two IS elements, 1000-1500 and 2000-3000. The bps4IS is the total size of two IS elements: bps4IS = (1500-1000+1 + 3000-2000+1 = 501 + 1001 = 1502 dnaLen = 5000 %Genome = 100 bps4IS/dnaLen = 100 1502/5000 = 30%

Hope it is clear for you.

Xie